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Sailo CV, Pandey P, Mukherjee S, Zami Z, Lalremruata R, Nemi L, Kumar NS. Pathogenic microbes contaminating mobile phones in hospital environment in Northeast India: incidence and antibiotic resistance. Trop Med Health 2019; 47:59. [PMID: 31889887 PMCID: PMC6905087 DOI: 10.1186/s41182-019-0190-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The present study attempts to identify and determine the pattern of drug susceptibility of the microorganisms present in mobile phones of health care workers (HCWs) and non-HCWs in a hospital environment. Mobile phones of 100 participants including both genders were randomly swabbed from nine different wards/units and the bacterial cultures were characterized using VITEK 2 system. RESULTS Forty-seven mobile phones were culture positive and a total of 57 isolates were obtained which consisted of 28 Gram-positive organisms and 29 Gram-negative organisms. The predominating organisms were Acinetobacter baumannii and Staphylococcus hominis. Among all the isolates from the mobile phones of HCW and non-HCWs, five isolates had ESBL and three isolates had colistin resistance. Incidentally, MRSA was not found on the mobile phones tested. The isolated organisms showed 100% susceptibility to linezolid, daptomycin, vancomycin, imipenem, meropenem, gentamicin, amikacin, ciprofloxacin and tigecycline, while high resistance was shown against benzylpenicillin (75.0%), cefuroxime and cefuroxime axetil (56.5%). Non-HCWs' mobile phones were more contaminated as compared to HCWs (P = 0.001) and irrespective of individuals' gender or toilet habits, both Gram-positive and Gram-negative organisms were present on the mobile phones. CONCLUSION This study reports for the first time that the mobile phones of non-health care workers harbour more bacterial diversity and are more prone to cause transmission of pathogens. This study can serve to educate the public on personal hand hygiene practices and on maintaining clean mobile phones through antiseptic measures.
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Affiliation(s)
| | - Puja Pandey
- 0000 0000 9217 3865grid.411813.eDepartment of Biotechnology, Mizoram University, Aizawl, Mizoram 796004 India
| | - Subhajit Mukherjee
- 0000 0000 9217 3865grid.411813.eDepartment of Biotechnology, Mizoram University, Aizawl, Mizoram 796004 India
| | - Zothan Zami
- 0000 0000 9217 3865grid.411813.eDepartment of Biotechnology, Mizoram University, Aizawl, Mizoram 796004 India
| | - Ralte Lalremruata
- grid.460962.fDepartment of Microbiology, Synod Hospital, Durtlang, Aizawl, Mizoram 796025 India
| | - Lalnun Nemi
- grid.460962.fDepartment of Pathology, Synod Hospital, Durtlang, Aizawl, Mizoram 796025 India
| | - Nachimuthu Senthil Kumar
- 0000 0000 9217 3865grid.411813.eDepartment of Biotechnology, Mizoram University, Aizawl, Mizoram 796004 India
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Neckovic A, van Oorschot RAH, Szkuta B, Durdle A. Investigation of direct and indirect transfer of microbiomes between individuals. Forensic Sci Int Genet 2019; 45:102212. [PMID: 31812098 DOI: 10.1016/j.fsigen.2019.102212] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 01/16/2023]
Abstract
The human microbiome encompasses the fungi, bacteria and viruses that live on, within, and immediately surrounding the body. Microbiomes have potential utility in forensic science as an evidentiary tool to link or exclude persons of interest associated with criminal activities. Research has shown the microbiome is individualised, and that personal microbial signatures can be recovered from surfaces such as phones, shoes and fabrics. Before the human microbiome may be used as an investigative tool, further research is required to investigate the utility and potential limitations surrounding microbial profiling. This includes the detectability of microbial transfer between individuals or items, the associated risks (such as contamination events) and the applicability of microbial profiling for forensic purposes. This research aimed to identify whether an individual's distinguishable microbiome could be transferred to another individual and onto substrates, and vice versa. Paper, cotton, and glass surfaces were chosen to represent a range of substrate matrices. The study involved six participants placed into three pairs; participants took part in two modes of transfer. Transfer Mode 1 involved the pair shaking hands, followed by rubbing a substrate in their right hand. Transfer Mode 2 involved individuals rubbing a substrate in their left hand, swapping substrates with their partner and then rubbing the swapped substrate in their left hand. 16S rRNA sequencing was performed on the extracted microbial DNA from participant and substrate samples. Quantitative Insights into Microbial Ecology 2 (QIIME 2) was used for sequence quality control and beta (between-sample) diversity analyses and taxonomic assignment. Principal Coordinate Analysis (PCoA) based on Jaccard distances was visualised through Emperor software to determine the phylogenetic similarity of bacterial communities between participants and among participant pairs. Statistical testing through PERMANOVA revealed significant differences in the Jaccard distances between each participant pair (P < 0.001), highlighting not only the potential distinguishability of skin microbiomes among individuals, but also the clustering effect observed between participant pairs due to the potential transfer of hand-associated microbiomes between individuals. The study demonstrated that transfer of the human skin microbiome had occurred between all participant pairs, regardless of substrate type or mode of transfer.
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Affiliation(s)
- Ana Neckovic
- Deakin University, School of Life and Environmental Sciences, Waurn Ponds, Australia.
| | - Roland A H van Oorschot
- Victoria Police Forensic Services Centre, Office of the Chief Forensic Scientist, Macleod, Australia; School of Molecular Sciences, La Trobe University, Bundoora, Australia
| | - Bianca Szkuta
- Deakin University, School of Life and Environmental Sciences, Waurn Ponds, Australia; Victoria Police Forensic Services Centre, Office of the Chief Forensic Scientist, Macleod, Australia
| | - Annalisa Durdle
- Deakin University, School of Life and Environmental Sciences, Waurn Ponds, Australia
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Amanah A, Apriyanto DR, Fitriani H. Isolation of Surveillance Pathogenic Fungal Microbial Contaminant on Mobile Phone. Open Access Maced J Med Sci 2019; 7:3393-3396. [PMID: 32002059 PMCID: PMC6980825 DOI: 10.3889/oamjms.2019.685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022] Open
Abstract
AIM Mobile phone has been used daily by almost everyone. This Research surveyed microbial contamination of mobile phones in the faculty of Medicine Universitas Swadaya Gunung Jati and identify the most influential fungal microbial species. METHODS A group of 15 samples was analysed to identify fungal isolates. The mobile phones were swabbed firmly passing its touch screen using sterile swabs then inoculated into media for fungi. Frequency distribution of isolates was calculated. RESULTS There were fungal isolates as follows: Aspergillus Orchareus, Aspergillus flavus, Alternaria, Aspergillus niger, Penicillium sp., Cladosporium sp., Candida sp., Aspergillus Fumigatus, and Mucor sp. at the rate of 19, 6, 1, 3, 2, 10, 2, 52, 2%, respectively. CONCLUSION The research indicates that all mobile phones were considerably having microbial infection, mostly from humans' natural flora and also from the air and soil. This determines that it is necessary to sterilize hands prior to a contact with mobile phones since it could lead into disease transmission.
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Affiliation(s)
- Amanah Amanah
- Faculty of Medicine, Universitas Swadaya Gunung Jati, Jl. Terusan Pemuda No.1A Cirebon, Cirebon, Indonesia
| | - Dadan Ramadhan Apriyanto
- Faculty of Medicine, Universitas Swadaya Gunung Jati, Jl. Terusan Pemuda No.1A Cirebon, Cirebon, Indonesia
| | - Hikmah Fitriani
- Faculty of Medicine, Universitas Swadaya Gunung Jati, Jl. Terusan Pemuda No.1A Cirebon, Cirebon, Indonesia
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Masuda-Kuroki K, Murakami M, Tokunaga N, Kishibe M, Mori H, Utsunomiya R, Tsuda T, Shiraishi K, Tohyama M, Sayama K. The microbiome of the "sterile" pustules in palmoplantar pustulosis. Exp Dermatol 2019; 27:1372-1377. [PMID: 30281856 DOI: 10.1111/exd.13791] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/11/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022]
Abstract
The skin microbiome influences skin pathophysiology. Palmoplantar pustulosis (PPP) is a chronic skin disease characterized by infectious-like pustules on the palms and soles. These pustules are thought to be sterile because bacterial cultures obtained from the pustules are negative. However, culture methods are limited in their ability to identify all bacteria on the skin. We hypothesized that the "sterile" pustules of PPP do not lack bacteria, but rather contain a microbiome. To test this hypothesis, we identified bacteria in "sterile" pustules using non-culture methods. We conducted Sanger and 16S rRNA sequencing using primers specific to the V1-V2 region in PPP-pustulovesicles (PVs) (n = 43) and pompholyx vesicle fluids (n = 15). Sanger sequencing identified some Staphylococcus, Propionibacterium, Streptococcus and Pyrinomonas species in PPP-PVs but failed to identify any bacteria in most of the pompholyx vesicles. 16S rRNA sequencing of PPP-PVs indicated the presence of a microbiome that included various phyla, including Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. At the genus level, smokers had higher levels of Staphylococcus in PPP-PVs compared with non-smokers. These results indicate that a microbiome exists in "sterile" pustules of PPP and that PPP smokers had higher levels of Staphylococcus in pustules. It is therefore necessary to reconsider the pathogenesis of PPP from the perspective of the microbiome.
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Affiliation(s)
- Kana Masuda-Kuroki
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Masamoto Murakami
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Naohito Tokunaga
- Advanced Research Support Center, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Mari Kishibe
- Department of Dermatology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Hideki Mori
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Ryo Utsunomiya
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Teruko Tsuda
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Ken Shiraishi
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Mikiko Tohyama
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
| | - Koji Sayama
- Department of Dermatology, Ehime University Graduate School of Medicine, Shitsukawa, Toon City, Ehime, Japan
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Impacts of silver-coated antimicrobial screen covers on the cell-phone microbiome of resident physicians. Infect Control Hosp Epidemiol 2019; 40:1427-1429. [PMID: 31631832 DOI: 10.1017/ice.2019.280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An antimicrobial screen was applied to the cell phones of 26 resident physicians to determine its effects on the phone microbiome and its potential to serve as a selective agent for antibiotic or silver resistance genes. No increase of these genes was observed now was there a shift in the overall microbial community.
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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Ribeiro LF, Lopes EM, Kishi LT, Ribeiro LFC, Menegueti MG, Gaspar GG, Silva-Rocha R, Guazzaroni ME. Microbial Community Profiling in Intensive Care Units Expose Limitations in Current Sanitary Standards. Front Public Health 2019; 7:240. [PMID: 31555629 PMCID: PMC6724580 DOI: 10.3389/fpubh.2019.00240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/12/2019] [Indexed: 11/30/2022] Open
Abstract
Hospital-associated infections (HAIs) are a leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiota may vary across different ICUs, the HAI-related microbial signatures within these units remain underexplored. In this study, we use deep-sequencing analyses to explore and compare the structure of bacterial communities at inanimate surfaces of the ICU and NICU wards of The Medical School Clinics Hospital (Brazil). The data revealed that NICU presents higher biodiversity than ICU and surfaces closest to the patient showed a peculiar microbiota, distinguishing one unit from the other. Several facultative anaerobes or obligate anaerobes HAI-related genera were classified as biomarkers for the NICU, whereas Pseudomonas was the main biomarker for ICU. Correlation analyses revealed a distinct pattern of microbe-microbe interactions for each unit, including bacteria able to form multi-genera biofilms. Furthermore, we evaluated the effect of concurrent cleaning over the ICU bacterial community. The results showed that, although some bacterial populations decreased after cleaning, various HAI-related genera were quite stable following sanitization, suggesting being well-adapted to the ICU environment. Overall, these results enabled identification of discrete ICU and NICU reservoirs of potentially pathogenic bacteria and provided evidence for the presence of a set of biomarkers genera that distinguish these units. Moreover, the study exposed the inconsistencies of the routine cleaning to minimize HAI-related genera contamination.
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Affiliation(s)
| | - Erica M Lopes
- Department of Cellular and Molecular Biology, FMRP -University of São Paulo, Ribeirao Preto, Brazil
| | - Luciano T Kishi
- National Laboratory of Scientific Computing, Petrópolis, Brazil
| | | | - Mayra Gonçalves Menegueti
- Infection Control Service, The Medical School Clinics Hospital, University of São Paulo, Ribeirao Preto, Brazil
| | - Gilberto Gambero Gaspar
- Infection Control Service, The Medical School Clinics Hospital, University of São Paulo, Ribeirao Preto, Brazil
| | - Rafael Silva-Rocha
- Department of Cellular and Molecular Biology, FMRP -University of São Paulo, Ribeirao Preto, Brazil
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Burcham ZM, Cowick CA, Baugher CN, Pechal JL, Schmidt CJ, Rosch JW, Benbow ME, Jordan HR. Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition. J Forensic Sci 2019; 64:1707-1719. [DOI: 10.1111/1556-4029.14083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/25/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Zachary M. Burcham
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Caitlyn A. Cowick
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Courtney N. Baugher
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
| | - Jennifer L. Pechal
- Department of Entomology Michigan State University 288 Farm Ln #243 East Lansing MI 48824
| | - Carl J. Schmidt
- Department of Pathology University of Michigan Medical Science Unit I, 1301 Catherine St Ann Arbor MI 48109
| | - Jason W. Rosch
- Department of Infectious Disease St. Jude Children's Research Hospital 262 Danny Thomas Place Memphis TN 38105
| | - M. Eric Benbow
- Department of Entomology Michigan State University 288 Farm Ln #243 East Lansing MI 48824
- Department of Osteopathic Medical Specialties Michigan State University West Fee Hall, 909 Fee Road East Lansing MI 48824
| | - Heather R. Jordan
- Department of Biological Sciences Mississippi State University PO Box GY Mississippi State MS 39762
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Díez López C, Vidaki A, Ralf A, Montiel González D, Radjabzadeh D, Kraaij R, Uitterlinden AG, Haas C, Lao O, Kayser M. Novel taxonomy-independent deep learning microbiome approach allows for accurate classification of different forensically relevant human epithelial materials. Forensic Sci Int Genet 2019; 41:72-82. [PMID: 31003081 DOI: 10.1016/j.fsigen.2019.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and identification when using previously proposed human cell biomarkers, while their microbiota composition largely differs. By using validated 16S rRNA gene massively parallel sequencing data from the Human Microbiome Project of 1636 skin, oral and vaginal samples, 50 taxonomy-independent deep learning networks were trained to classify these three tissues. Validation testing was performed in de-novo generated high-throughput 16S rRNA gene sequencing data using the Ion Torrent™ Personal Genome Machine from 110 test samples: 56 hand skin, 31 saliva and 23 vaginal secretion specimens. Body-site classification accuracy of these test samples was very high as indicated by AUC values of 0.99 for skin, 0.99 for oral, and 1 for vaginal secretion. Misclassifications were limited to 3 (5%) skin samples. Additional forensic validation testing was performed in mock casework samples by de-novo high-throughput sequencing of 19 freshly-prepared samples and 22 samples aged for 1 up to 7.6 years. All of the 19 fresh and 20 (91%) of the 22 aged mock casework samples were correctly tissue-type classified. Moreover, comparing the microbiome results with outcomes from previous human mRNA-based tissue identification testing in the same 16 aged mock casework samples reveals that our microbiome approach performs better in 12 (75%), similarly in 2 (12.5%), and less good in 2 (12.5%) of the samples. Our results demonstrate that this new microbiome approach allows for accurate tissue-type classification of three human epithelial materials of skin, oral and vaginal origin, which is highly relevant for future forensic investigations.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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Bodena D, Teklemariam Z, Balakrishnan S, Tesfa T. Bacterial contamination of mobile phones of health professionals in Eastern Ethiopia: antimicrobial susceptibility and associated factors. Trop Med Health 2019; 47:15. [PMID: 30858754 PMCID: PMC6391816 DOI: 10.1186/s41182-019-0144-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/14/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mobile phones of health care professionals could harbor microbes which cause nosocomial infections to the patient, family members, and the community at large. Thus, the aim of this study was to determine the prevalence of bacterial contamination of the mobile phones of health professionals, identify bacterial isolates, assess their antimicrobial susceptibility patterns, and define the associated factors. METHOD A cross-sectional study was conducted from February to March 2018 on 226 health professionals' mobile phones which were selected by a simple random sampling technique. Data were collected using a self-administered questionnaire. A swab sample from each of health professional's mobile phone device was collected and transported to the microbiology laboratory for bacterial culture and antimicrobial susceptibility tests. Data were entered into EpiData version 3.1 and analyzed by using the Statistical Package for Social Sciences (SPSS) program version 20. RESULT The overall prevalence of mobile phone contamination with one or more bacteria was 94.2%. Coagulase-negative staphylococci (CoNS; 58.8%), Staphylococcus aureus (14.4%), and Klebsiella species (6.9%) were the most predominant bacterial isolates. The overall prevalence of multidrug-resistant bacteria was 69.9%. About half of Gram-positive and Gram-negative bacteria were resistant to ampicillin and trimethoprim-sulfamethoxazole. Male sex (adjusted odds ratio (AOR) 4.1, 95% confidence interval (CI) 1.1, 15.8) and the absence of regular phone cleaning/disinfecting were found to be the most significant factors (AOR 4.1, 95% CI 1.2, 13.5) associated with health care professionals' mobile phone bacterial contamination. CONCLUSION There is a high contamination rate of mobile phones with nosocomial pathogens. Most of the isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole and also multidrug-resistant. A mobile phone belonging to male health professionals and to those not disinfecting mobile phones was significantly contaminated with bacteria. Therefore, strategies for preventing nosocomial transmission of drug-resistant pathogens through mobile phones, like hand washing and cleaning mobile phones, are recommended.
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Affiliation(s)
- Dagne Bodena
- 0000 0001 0108 7468grid.192267.9Hiwot Fana Specialized University Hospital, College of Health and Medical Sciences, Haramaya University, P.O. box 235, Harar, Ethiopia
| | - Zelelam Teklemariam
- 0000 0001 0108 7468grid.192267.9Department of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, P.O. box 235, Harar, Ethiopia
| | - Senthilkumar Balakrishnan
- 0000 0001 0108 7468grid.192267.9Department of Medical Microbiology, College of Health and Medical Sciences, Haramaya University, P.O. box 235, Harar, Ethiopia
| | - Tewodros Tesfa
- 0000 0001 0108 7468grid.192267.9Department of Medical Laboratory Sciences, College of Health and Medical Sciences, Haramaya University, P.O. box 235, Harar, Ethiopia
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Parthasarathy A, Wong NH, Weiss AN, Tian S, Ali SE, Cavanaugh NT, Chinsky TM, Cramer CE, Gupta A, Jha R, Johnson LK, Tuason ED, Klafehn LM, Krishnadas V, Musich RJ, Pfaff JM, Richman SC, Shumway AJ, Hudson AO. SELfies and CELLfies: Whole Genome Sequencing and Annotation of Five Antibiotic Resistant Bacteria Isolated from the Surfaces of Smartphones, An Inquiry Based Laboratory Exercise in a Genomics Undergraduate Course at the Rochester Institute of Technology. J Genomics 2019; 7:26-30. [PMID: 30820259 PMCID: PMC6389494 DOI: 10.7150/jgen.31911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/06/2023] Open
Abstract
Are touchscreen devices a public health risk for the transmission of pathogenic bacteria, especially those that are resistant to antibiotics? To investigate this, we embarked on a project aimed at isolating and identifying bacteria that are resistant to antibiotics from the screens of smartphones. Touchscreen devices have become ubiquitous in society, and it is important to evaluate the potential risks they pose towards public health, especially as it pertains to the harboring and transmission of pathogenic bacteria that are resistant to antibiotics. Sixteen bacteria were initially isolated of which five were unique (four Staphylococcus species and one Micrococcus species). The genomes of the five unique isolates were subsequently sequenced and annotated. The genomes were analyzed using in silico tools to predict the synthesis of antibiotics and secondary metabolites using the antibiotics and Secondary Metabolite Analysis SHell (antiSMASH) tool in addition to the presence of gene clusters that denote resistance to antibiotics using the Resistance Gene Identifier (RGI) tool. In vivo analysis was also done to assess resistance/susceptibility to four antibiotics that are commonly used in a research laboratory setting. The data presented in this manuscript is the result of a semester-long inquiry based laboratory exercise in the genomics course (BIOL340) in the Thomas H. Gosnell School of Life Sciences/College of Science at the Rochester Institute of Technology.
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Affiliation(s)
- Anutthaman Parthasarathy
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Narayan H Wong
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Amanda N Weiss
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Susan Tian
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Sara E Ali
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Nicole T Cavanaugh
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Tyler M Chinsky
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Chelsea E Cramer
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Aditya Gupta
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Rakshanda Jha
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Loryn K Johnson
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Elizabeth D Tuason
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Lauren M Klafehn
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Varada Krishnadas
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Ryan J Musich
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Jennifer M Pfaff
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Spencer C Richman
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - Alexandria J Shumway
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
| | - André O Hudson
- The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA
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Merino N, Zhang S, Tomita M, Suzuki H. Comparative genomics of Bacteria commonly identified in the built environment. BMC Genomics 2019; 20:92. [PMID: 30691394 PMCID: PMC6350394 DOI: 10.1186/s12864-018-5389-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles. RESULTS Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes." CONCLUSION Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Department of Earth Sciences, University of Southern California, Stauffer Hall of Science, Los Angeles, CA, 90089, USA
| | - Shu Zhang
- Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Material Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan.,Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, 90089-0641, USA
| | - Masaru Tomita
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0035, Japan
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan. .,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0035, Japan.
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64
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Jansen AS, Balbinot GC, Daur AV, da Silva ACF, Nogueira KS, Fernandes T, Marconi C. Detection of potentially pathogenic bacteria on cell phones of hospital and university-based populations in Curitiba, southern Brazil. A cross-sectional study. SAO PAULO MED J 2019; 137:343-348. [PMID: 31553361 PMCID: PMC9744018 DOI: 10.1590/1516-3180.2018.044305072019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/05/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cell phones have become indispensable for professional activities, including healthcare. Thus, they are possible sources of bacterial contamination. There is a scarcity of data in the literature regarding identification of risk factors for contamination of cell phones with pathogenic bacteria. OBJECTIVE To compare the prevalence rates of Staphylococcus aureus (S. aureus), methicillin-resistant S. aureus (MRSA) and/or Enterobacteriaceae on cell phones belonging to hospital healthcare staff and university students in Curitiba, Paraná, Brazil, and to identify variables associated with such contamination. DESIGN AND SETTING Cross-sectional study conducted in a public university's referral hospital and lecture buildings in 2017. METHODS We sampled the surface of cell phones using the dipslide method, with Baird-Parker agar and Escherichia coli-coliform chromogenic (ECC) agar. We assessed the population's sociodemographic, behavioral and hygiene characteristics through interviews. Possible presence of S. aureus colonies was confirmed using agglutination tests, with evaluation of methicillin sensitivity. Colonies in ECC medium were counted. Stepwise logistic regression (forward P < 0.15) was performed to identify characteristics associated with bacterial contamination. RESULTS The prevalence rates of S. aureus, MRSA and Enterobacteriaceae were, respectively, 32%, 4% and 3%. No difference was found between the hospital and university-based populations (P > 0.05). The only variable associated with bacterial contamination was the use of cloth/velvet/leather phone cases (odds ratio: 2.92; 95% confidence interval: 1.08-7.91). CONCLUSIONS Potentially pathogenic bacteria were prevalent on the cell phones of this hospital and university population. Use of phone cases made of cloth-like material should be discouraged, especially in hospital settings.
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Affiliation(s)
- Andressa Siqueira Jansen
- Undergraduate Student, Biomedical Sciences Course, Universidade Federal do Paraná (UFPR), Curitiba (PR), Brazil.
| | - Giuliano Carlo Balbinot
- Undergraduate Student, Biomedical Sciences Course, Universidade Federal do Paraná (UFPR), Curitiba (PR), Brazil.
| | - Alessandra Vale Daur
- MSc. Technical Manager, Laborclin Produtos para Laboratórios, Pinhais (PR), Brazil.
| | | | - Keite Silva Nogueira
- PhD. Adjunct Professor, Department of Basic Pathology, Universidade Federal do Paraná (UFPR), Curitiba (PR), Brazil.
| | - Thaiz Fernandes
- BSc. Master’s Student, Postgraduate Program, Department of Basic Pathology, Universidade Federal do Paraná (UFPR), Curitiba (PR), Brazil.
| | - Camila Marconi
- PhD. Adjunct Professor, Department of Basic Pathology, Universidade Federal do Paraná (UFPR), Curitiba (PR), Brazil.
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65
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Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB. Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue. J Forensic Sci 2018; 64:791-798. [PMID: 30408195 DOI: 10.1111/1556-4029.13949] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/29/2022]
Abstract
Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin microbiomes change prior to autopsy and, if so, whether these changes interfere with linking objects to decedents. The current study included microbiomes from 16 scenes of death in the City and County of Honolulu and tested whether objects at the scenes can be linked to individual decedents. Postmortem skin microbiomes were stable during repeated sampling up to 60 h postmortem and were similar to microbiomes of an antemortem population. Objects could be traced to decedents approximately 75% of the time, with smoking pipes and medical devices being especially accurate (100% match), house and car keys being poor (0%), and other objects like phones intermediate (~80%). These results show that microbes from objects at death scenes can be matched to individual decedents, opening up a new method of establishing associations and identifications.
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Affiliation(s)
- Whitney A Kodama
- City and County of Honolulu Department of the Medical Examiner, 835 Iwilei Street, Honolulu, 96817, HI.,Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, 96816, HI
| | - Zhenjiang Xu
- School of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang City, Jiangxi, Nanchang, China.,State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang City, Jiangxi, Nanchang, China.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, 350 W. Pitkin Street, Ft. Collins, 80523-1171, CO
| | - Se Jin Song
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA
| | - Nicholas Harrison
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, 96816, HI
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA.,Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093, CA.,Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0403, CA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, 3140 Waialae Avenue, Honolulu, 96816, HI
| | - Christopher B Happy
- City and County of Honolulu Department of the Medical Examiner, 835 Iwilei Street, Honolulu, 96817, HI
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66
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Oliveira M, Amorim A. Microbial forensics: new breakthroughs and future prospects. Appl Microbiol Biotechnol 2018; 102:10377-10391. [PMID: 30302518 PMCID: PMC7080133 DOI: 10.1007/s00253-018-9414-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 12/17/2022]
Abstract
Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancillary evidence in criminal cases; (ii) to clarify causes of death (e.g., drownings, toxicology, hospital-acquired infections, sudden infant death and shaken baby syndromes); (iii) to assist human identification (skin, hair and body fluid microbiomes); (iv) for geolocation (soil microbiome); and (v) to estimate postmortem interval (thanatomicrobiome and epinecrotic microbial community). When compared with classical microbiological methods, MPS offers a diverse range of advantages and alternative possibilities. However, prior to its implementation in the forensic context, critical efforts concerning the elaboration of standards and guidelines consolidated by the creation of robust and comprehensive reference databases must be undertaken.
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal.
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal
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67
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Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC. Interaction between the microbiome and TP53 in human lung cancer. Genome Biol 2018; 19:123. [PMID: 30143034 PMCID: PMC6109311 DOI: 10.1186/s13059-018-1501-6] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/02/2018] [Indexed: 12/19/2022] Open
Abstract
Background Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort. Results Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas. Conclusions The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection. Electronic supplementary material The online version of this article (10.1186/s13059-018-1501-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K Leigh Greathouse
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA.,Present Address: Nutrition Sciences, Baylor University, Waco, TX, 97346, USA
| | | | - Ashely J Vargas
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Valery V Bliskovsky
- Center for Cancer Research Genomics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jessica A Beck
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Natalia von Muhlinen
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Eric C Polley
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Mohammed A Khan
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Tomer Cooks
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA
| | - Noah Padgett
- Department of Educational Psychology, Baylor University, Waco, TX, 97346, USA
| | - Amiran H Dzutsev
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Giorgio Trinchieri
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marbin A Pineda
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Sven Bilke
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, Bethesda, MD, 20892, USA
| | - Alexis N Hokenstad
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | | | - Marina R Walther-Antonio
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA.,Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joshua P Earl
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Joshua C Mell
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Jaroslaw E Krol
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Sergey V Balashov
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Archana S Bhat
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Alex Valm
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Clayton Deming
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sean Conlan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia Oh
- Jackson Laboratory, Framingham, CT, 06032, USA
| | - Julie A Segre
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer, Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Rm 3068A, MSC 4258, Bethesda, MD, 20892-4258, USA.
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Zhang N, Li Y. Transmission of Influenza A in a Student Office Based on Realistic Person-to-Person Contact and Surface Touch Behaviour. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:E1699. [PMID: 30096894 PMCID: PMC6121424 DOI: 10.3390/ijerph15081699] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022]
Abstract
Influenza A viruses result in the deaths of hundreds of thousands of individuals worldwide each year. In this study, influenza A transmission in a graduate student office is simulated via long-range airborne, fomite, and close contact routes based on real data from more than 3500 person-to-person contacts and 127,000 surface touches obtained by video-camera. The long-range airborne, fomite and close contact routes contribute to 54.3%, 4.2% and 44.5% of influenza A infections, respectively. For the fomite route, 59.8%, 38.1% and 2.1% of viruses are transmitted to the hands of students from private surfaces around the infected students, the students themselves and other susceptible students, respectively. The intranasal dose via fomites of the students' bodies, belongings, computers, desks, chairs and public facilities are 8.0%, 6.8%, 13.2%, 57.8%, 9.3% and 4.9%, respectively. The intranasal dose does not monotonously increase or decrease with the virus transfer rate between hands and surfaces. Mask wearing is much more useful than hand washing for control of influenza A in the tested office setting. Regular cleaning of high-touch surfaces, which can reduce the infection risk by 2.14%, is recommended and is much more efficient than hand-washing.
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Affiliation(s)
- Nan Zhang
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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69
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Kurli R, Chaudhari D, Pansare AN, Khairnar M, Shouche YS, Rahi P. Cultivable Microbial Diversity Associated With Cellular Phones. Front Microbiol 2018; 9:1229. [PMID: 29930546 PMCID: PMC6000418 DOI: 10.3389/fmicb.2018.01229] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this study, we investigated the diversity of microorganisms associated with cellular phones of 27 individuals using cultivation-based methods. Cellular phones were sampled using cotton swabs and a total of 554 isolates representing different morphotypes were obtained on four growth media. Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry could generate protein profiles for 527 isolates and species-level identification was obtained for 415 isolates. A dendrogram was constructed based on the protein profiles of the remaining isolates, to group 112 isolates under 39 different proteotypes. The representative strains of each group were selected for 16S rRNA gene and ITS region sequencing based identification. Staphylococcus, Bacillus, Micrococcus, and Pseudomonas were the most frequently encountered bacteria, and Candida, Aspergillus, Aureobasidium, and Cryptococcus were in case of fungi. At species-level the prevalence of Micrococcus luteus, Staphylococcus hominis, Staphylococcus epidermidis, Staphylococcus arlettae, Bacillus subtilis, and Candida parapsilosis was observed, most of these species are commensal microorganisms of human skin. UPGMA dendrogram and PCoA biplot generated based on the microbial communities associated with all cellular phones exhibited build-up of specific communities on cellular phones and the prevalence of objectionable microorganisms in some of the cellular phones can be attributed to the poor hygiene and sanitary practices. The study also revealed the impact of MALDI-TOF MS spectral quality on the identification results. Overall MALDI-TOF appears a powerful tool for routine microbial identification and de-replication of microorganisms. Quality filtering of MALDI-TOF MS spectrum, development of better sample processing methods and enriching the spectral database will improve the role of MALDI-TOF MS in microbial identifications.
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Affiliation(s)
- Rashmi Kurli
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Diptaraj Chaudhari
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Aabeejjeet N Pansare
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
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Lando AM, Bazaco MC, Chen Y. Consumers' Use of Personal Electronic Devices in the Kitchen. J Food Prot 2018; 81:437-443. [PMID: 29474153 DOI: 10.4315/0362-028x.jfp-17-172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 11/07/2017] [Indexed: 11/11/2022]
Abstract
Smartphones, tablets, and other personal electronic devices have become ubiquitous in Americans' daily lives. These devices are used by people throughout the day, including while preparing food. For example, a device may be used to look at recipes and therefore be touched multiple times during food preparation. Previous research has indicated that cell phones can harbor bacteria, including opportunistic human pathogens such as Staphylococcus and Klebsiella spp. This investigation was conducted with data from the 2016 Food Safety Survey (FSS) and from subsequent focus groups to determine the frequency with which consumers use personal electronic devices in the kitchen while preparing food, the types of devices used, and hand washing behaviors after handling these devices. The 2016 FSS is the seventh wave of a repeated cross-sectional survey conducted by the U.S. Food and Drug Administration in collaboration with the U.S. Department of Agriculture. The goal of the FSS is to evaluate U.S. adult consumer attitudes, behaviors, and knowledge about food safety. The FSS included 4,169 adults that were contacted using a dual-frame (land line and cell phone interviews) random-digit-dial sampling process. The personal electronics module was the first of three food safety topics discussed by each of eight consumer focus groups, which were convened in four U.S. cities in fall 2016. Results from the 2016 FSS revealed that of those individuals who use personal electronic devices while cooking, only about one third reported washing hands after touching the device and before continuing cooking. This proportion is significantly lower than that for self-reported hand washing behaviors after touching risky food products such as raw eggs, meat, chicken, or fish. Results from the focus groups highlight the varied usage of these devices during food preparation and the related strategies consumers are using to incorporate personal electric devices into their cooking routines.
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Affiliation(s)
- Amy M Lando
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, Maryland 20740, USA
| | - Michael C Bazaco
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, Maryland 20740, USA
| | - Yi Chen
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, Maryland 20740, USA
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Rahi P, Kurli R, Pansare AN, Khairnar M, Jagtap S, Patel NB, Dastager SG, Lawson PA, Shouche YS. Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone. Int J Syst Evol Microbiol 2018; 68:1052-1058. [PMID: 29458489 DOI: 10.1099/ijsem.0.002622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A cultivation-based study of the microbial diversity of cellular phone screens led to the isolation of a Gram-stain-positive, aerobic, rod-shaped and non-endospore-forming bacterium, designated S2T63T, exhibiting phenotypic and genotypic characteristics unique to the type strains of closely related species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a member of Microbacterium, and most closely related to Microbacterium aurantiacum IFO 15234T and Microbacterium kitamiense Kitami C2T. The DNA-DNA relatedness values of the strain S2T63T to M. aurantiacum KACC 20510T, M. kitamiense KACC 20514Tand Microbacterium laevaniformans KACC 14463T were 65 % (±4), 29.5 % (±3) and 55.9 % (±4), respectively. The genomic DNA G+C content was 71.8 mol%. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified polar lipids. The peptidoglycan contained the amino acids glycine, lysine, alanine and glutamic acid, with substantial amounts of hydroxy glutamic acid detected, which is characteristic of peptidoglycan type B1α. The predominant menaquinones were MK-12 and MK-13. Rhamnose, fucose and galactose were the whole-cell sugars detected. The strain also showed biofilm production, estimated by using crystal violet assay. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new strain represents a novel species of the genus Microbacterium, for which the name Microbacteriumtelephonicum is proposed, with S2T63T (=MCC 2967T=KACC 18715T=LMG 29293T) as the type strain.
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Affiliation(s)
- Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Rashmi Kurli
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Aabeejjeet N Pansare
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Mitesh Khairnar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Shubhangi Jagtap
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Nisha B Patel
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Syed G Dastager
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, Maharashtra 411007, India
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72
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Affiliation(s)
- Prabha Desikan
- Bhopal Memorial Hospital and Research Centre, Bhopal, Madhya Pradesh, India
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Hamdy AM, El-massry M, Kashef MT, Amin MA, Aziz RK. Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms. ACTA ACUST UNITED AC 2018; 22:133-144. [DOI: 10.1089/omi.2017.0091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Amal M. Hamdy
- Misr Company for Pharmaceutical Industries, Cairo, Egypt
| | - Moamen El-massry
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Magdy A. Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy K. Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Debnath T, Bhowmik S, Islam T, Hassan Chowdhury MM. Presence of Multidrug-Resistant Bacteria on Mobile Phones of Healthcare Workers Accelerates the Spread of Nosocomial Infection and Regarded as a Threat to Public Health in Bangladesh. J Microsc Ultrastruct 2018; 6:165-169. [PMID: 30221143 PMCID: PMC6130244 DOI: 10.4103/jmau.jmau_30_18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recently, mobile phones have become a potent vector for the transmission of pathogens. In hospitals, the use of the mobile phones by healthcare workers in an unhygienic manner accelerates the spread of nosocomial infection. We aimed to investigate the prevalence of microbiological contamination of mobile phones belonging to clinicians in Bangladesh hospitals. From 100 samples, we identified 69 isolates of bacteria including 22 Staphylococcus aureus; 11 Pseudomonas aeruginosa; 14 Escherichia coli; 6 Salmonella typhi 6 and 16 Staphylococcus epidermidis. On the basis of antibiotic susceptibility test using 11 antibiotics, it has been observed that most of the isolated bacteria became resistant to antibiotics and compared to other isolates, isolates of S. epidermidis and S. typhi were more resistant and sensitive, respectively. About 68.8% isolates showed that their resistance capacities against ampicillin but in contrast, 56.6% isolated were susceptible to imipenem. Azithromycin and imipenem against S. aureus, gentamicin against P. aeruginosa, tetracycline and imipenem against E. coli, tetracycline against S. typhi, and S. epidermidis revealed significant antimicrobial affectivity. We found that mobile phones are potential vectors to spread antibiotic-resistant nosocomial pathogens. Based on the study, an effective disinfection practice for cellular phones used in hospitals should be introduced to prevent the potential of cross-contamination.
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Affiliation(s)
- Tonmoy Debnath
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung City, Taiwan
| | - Shukanta Bhowmik
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Tarequl Islam
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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Microbial Forensics: Beyond a Fascination. DNA FINGERPRINTING: ADVANCEMENTS AND FUTURE ENDEAVORS 2018. [PMCID: PMC7121623 DOI: 10.1007/978-981-13-1583-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microbiology has seen a great transition from culture-based identification of microbes using various biochemical and microscopic observations to identify and functionally characterize the microbes by just collecting the DNA and sequencing it. This advancement has not only moved in and around microbiology but has found its applications in fields which were earlier considered to be the remote ones. Forensics is one such field, where tracing the leftover evidence on a crime scene can lead to the identification and prosecution of the culprit. When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—“microbial forensics.” Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Studies have supported the assumption that skin or surface microflora of an individual is somewhat related with the microflora found on the objects used by that individual and efforts are ongoing to see if this is found consistently in various surroundings and with different individuals. Once established, this technique would facilitate accurate identification and differentiation of an individual or suspect to guide investigations along with conventional evidence. Legal investigations are not only the field where microbial forensic could help. Agriculture, defense, public health, tourism, etc. are the fields wherein microbial forensics with different names based on the fields are helping out and have potential to further support other fields.
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Di Lodovico S, Del Vecchio A, Cataldi V, Di Campli E, Di Bartolomeo S, Cellini L, Di Giulio M. Microbial Contamination of Smartphone Touchscreens of Italian University Students. Curr Microbiol 2017; 75:336-342. [PMID: 29247337 DOI: 10.1007/s00284-017-1385-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]
Abstract
In this study, the microbial contamination of smartphones from Italian University students was analyzed. A total of 100 smartphones classified as low, medium, and high emission were examined. Bacteria were isolated on elective and selective media and identified by biochemical tests. The mean values of cfu/cm2 were 0.79 ± 0.01; in particular, a mean of 1.21 ± 0.12, 0.77 ± 0.1 and 0.40 ± 0.10 cfu/cm2 was present on smartphones at low, medium, and high emission, respectively. The vast majority of identified microorganisms came from human skin, mainly Staphylococci, together with Gram-negative and positive bacilli and yeasts. Moreover, the main isolated species and their mixture were exposed for 3 h to turned on and off smartphones to evaluate the effect of the electromagnetic wave emission on the bacterial cultivability, viability, morphology, and genotypic profile in respect to the unexposed broth cultures. A reduction rate of bacterial growth of 79 and 46% was observed in Staphylococcus aureus and Staphylococcus epidermidis broth cultures, respectively, in the presence of turned on smartphone. No differences in viability were observed in all detected conditions. Small colony variants and some differences in DNA fingerprinting were detected on bacteria when the smartphones were turned on in respect to the other conditions. The colonization of smartphones was limited to human skin microorganisms that can acquire phenotype and genotypic modifications when exposed to microwave emissions.
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Affiliation(s)
- Silvia Di Lodovico
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
| | - Angela Del Vecchio
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
| | - Valentina Cataldi
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
| | - Emanuela Di Campli
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
| | - Soraya Di Bartolomeo
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
| | - Luigina Cellini
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy.
| | - Mara Di Giulio
- Department of Pharmacy, "G. d'Annunzio" University, Chieti-Pescara, Via dei Vestini 31, 66100, Chieti Scalo, Italy
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Forensic Human Identification Using Skin Microbiomes. Appl Environ Microbiol 2017; 83:AEM.01672-17. [PMID: 28887423 DOI: 10.1128/aem.01672-17] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/02/2017] [Indexed: 01/09/2023] Open
Abstract
The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications; however, a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described here to classify skin microbiomes to their donors by comparing two feature types: Propionibacterium acnes pangenome presence/absence features and nucleotide diversities of stable clade-specific markers. Supervised learning was used to attribute skin microbiomes from 14 skin body sites from 12 healthy individuals sampled at three time points over a >2.5-year period with accuracies of up to 100% for three body sites. Feature selection identified a reduced subset of markers from each body site that are highly individualizing, identifying 187 markers from 12 clades. Classification accuracies were compared in a formal model testing framework, and the results of this analysis indicate that learners trained on nucleotide diversity perform significantly better than those trained on presence/absence encodings. This study used supervised learning to identify individuals with high accuracy and associated stable features from skin microbiomes over a period of up to almost 3 years. These selected features provide a preliminary marker panel for future development of a robust and reproducible method for skin microbiome profiling for forensic human identification.IMPORTANCE A novel approach is described to attribute skin microbiomes, collected over a period of >2.5 years, to their individual hosts with a high degree of accuracy. Nucleotide diversities of stable clade-specific markers with supervised learning were used to classify skin microbiomes from a particular individual with up to 100% classification accuracy for three body sites. Attribute selection was used to identify 187 genetic markers from 12 clades which provide the greatest differentiation of individual skin microbiomes from 14 skin sites. This study performs skin microbiome profiling from a supervised learning approach and obtains high classification accuracy for samples collected from individuals over a relatively long time period for potential application to forensic human identification.
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78
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Schmedes SE, Woerner AE, Novroski NMM, Wendt FR, King JL, Stephens KM, Budowle B. Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification. Forensic Sci Int Genet 2017; 32:50-61. [PMID: 29065388 DOI: 10.1016/j.fsigen.2017.10.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022]
Abstract
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb), and 100% (Hp) accuracy. All samples (n=72) regardless of body site origin were correctly classified with up to 94% accuracy, and body site origin could be predicted with up to 86% accuracy. Finally, human short tandem repeat and single-nucleotide polymorphism profiles were generated from skin swab extracts from a single subject to highlight the potential to use microbiome profiling in conjunction with low-biomass samples. The hidSkinPlex is a novel targeted enrichment approach to profile skin microbiomes for human forensic identification purposes and provides a method to further characterize the utility of skin microflora for human identification in future studies, such as the stability and diversity of the personal skin microbiome.
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Affiliation(s)
- Sarah E Schmedes
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Nicole M M Novroski
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Frank R Wendt
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | | | - Bruce Budowle
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
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79
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Debnath T, Bhowmik S, Islam T, Chowdhury MMH. Presence of multidrug resistant bacteria on mobile phones of healthcare workers accelerates the spread of nosocomial infections and regarded as a threat to public health in Bangladesh. J Microsc Ultrastruct 2017. [DOI: 10.1016/j.jmau.2017.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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80
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Prescott SL, Larcombe DL, Logan AC, West C, Burks W, Caraballo L, Levin M, Etten EV, Horwitz P, Kozyrskyj A, Campbell DE. The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming. World Allergy Organ J 2017; 10:29. [PMID: 28855974 PMCID: PMC5568566 DOI: 10.1186/s40413-017-0160-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 02/06/2023] Open
Abstract
Skin barrier structure and function is essential to human health. Hitherto unrecognized functions of epidermal keratinocytes show that the skin plays an important role in adapting whole-body physiology to changing environments, including the capacity to produce a wide variety of hormones, neurotransmitters and cytokine that can potentially influence whole-body states, and quite possibly, even emotions. Skin microbiota play an integral role in the maturation and homeostatic regulation of keratinocytes and host immune networks with systemic implications. As our primary interface with the external environment, the biodiversity of skin habitats is heavily influenced by the biodiversity of the ecosystems in which we reside. Thus, factors which alter the establishment and health of the skin microbiome have the potential to predispose to not only cutaneous disease, but also other inflammatory non-communicable diseases (NCDs). Indeed, disturbances of the stratum corneum have been noted in allergic diseases (eczema and food allergy), psoriasis, rosacea, acne vulgaris and with the skin aging process. The built environment, global biodiversity losses and declining nature relatedness are contributing to erosion of diversity at a micro-ecological level, including our own microbial habitats. This emphasises the importance of ecological perspectives in overcoming the factors that drive dysbiosis and the risk of inflammatory diseases across the life course.
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Affiliation(s)
- Susan L Prescott
- School of Paediatrics and Child Health, University of Western Australia and Princess Margaret Hospital for Children, PO Box D184, Perth, WA 6001 Australia.,In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA
| | - Danica-Lea Larcombe
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA.,School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Alan C Logan
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA
| | - Christina West
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA.,Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Wesley Burks
- University of North Carolina School of Medicine, Chapel Hill, North Carolina USA
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Michael Levin
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA.,Division of Paediatric Allergy, University of Cape Town, Cape Town, South Africa
| | - Eddie Van Etten
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Pierre Horwitz
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA 6027 Australia
| | - Anita Kozyrskyj
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA.,Department of Pediatrics, University of Alberta, Edmonton, Canada
| | - Dianne E Campbell
- In-FLAME Global Network, of the World Universities Network (WUN), West New York, USA.,Children's Hospital at Westmead, Sydney, Australia.,Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
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81
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Rahi P, Kurli R, Khairnar M, Jagtap S, Pansare AN, Dastager SG, Shouche YS. Description of Lysinibacillus telephonicus sp. nov., isolated from the screen of a cellular phone. Int J Syst Evol Microbiol 2017; 67:2289-2295. [PMID: 28699866 DOI: 10.1099/ijsem.0.001943] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, designated S5H2222T, was isolated form the screen of a cellular phone. The cells were Gram-stain-positive, rod-shaped, aerobic and motile, and endospores are formed. S5H2222T grew as pale white colonies on trypticase soy agar and the best growth was observed at 37 °C (10-55 °C) and at pH 7.0 (5.0-9.0). S5H2222T could tolerate up to 10 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences placed this strain within the genus Lysinibacillus and it exhibited high 16S rRNA gene sequence similarity to Lysinibacillus halotolerans LAM612T (97.8 %), Lysinibacillus chungkukjangi 2RL3-2T (97.4 %) and Lysinibacillus sinduriensis BLB-1T (97.2 %). The DNA-DNA relatedness of the strain with L. halotolerans JCM 19611T, L. chungkukjangi KACC 16626T and L. sinduriensis KACC 16611T was 57, 64 and 55 % respectively. The genomic DNA G+C content was 39.8 mol%. The major fatty acids of S5H2222T were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. MK-7 was the only menaquinone and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, four unidentified polar lipids were also present. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α). On the basis of the results of the phenotypic and genotypic characterizations, it was concluded that S5H2222T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus telephonicus sp. nov. is proposed. The type strain is S5H2222T (=MCC 3065T=KACC 18714T=LMG 29294T).
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Rashmi Kurli
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Mitesh Khairnar
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Shubhangi Jagtap
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Aabeejjeet N Pansare
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Syed G Dastager
- NCIM-Resource Center, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411007, India
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82
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Kõljalg S, Mändar R, Sõber T, Rööp T, Mändar R. High level bacterial contamination of secondary school students' mobile phones. Germs 2017. [PMID: 28626737 DOI: 10.18683/germs.2017.1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. METHODS Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline (tetA, tetB, tetM), erythromycin (ermB) and sulphonamide (sul1) resistance genes was assessed. RESULTS We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm2) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes (Staphylococcus aureus, Acinetobacter spp., Pseudomonas spp., Bacillus cereus and Neisseria flavescens) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. CONCLUSION Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.
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Affiliation(s)
- Siiri Kõljalg
- MD, PhD, Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - Rando Mändar
- School of Law, University of Tartu, Näituse 20, Tartu 50409, Estonia
| | - Tiina Sõber
- MSc, Tartu Kristjan Jaak Peterson Gymnasium, Kaunase puiestee 70, Tartu 50704, Estonia
| | - Tiiu Rööp
- MSc, Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - Reet Mändar
- MD, PhD, Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu. Ravila 19, Tartu 50411, Estonia
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Global-Scale Structure of the Eelgrass Microbiome. Appl Environ Microbiol 2017; 83:AEM.03391-16. [PMID: 28411219 PMCID: PMC5452814 DOI: 10.1128/aem.03391-16] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/05/2017] [Indexed: 02/06/2023] Open
Abstract
Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments. IMPORTANCE Plants depend critically on their associated microbiome, yet the structure of microbial communities found on marine plants remains poorly understood in comparison to that for terrestrial species. Seagrasses are the only flowering plants that live entirely in marine environments. The return of terrestrial seagrass ancestors to oceans is among the most extreme habitat shifts documented in plants, making them an ideal testbed for the study of microbial symbioses with plants that experience relatively harsh abiotic conditions. In this study, we report the results of a global sampling effort to extensively characterize the structure of microbial communities associated with the widespread seagrass species Zostera marina, or eelgrass, across its geographic range. Our results reveal major differences in the structure and composition of above- versus belowground microbial communities on eelgrass surfaces, as well as their relationships with the environment and host.
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Lax S, Sangwan N, Smith D, Larsen P, Handley KM, Richardson M, Guyton K, Krezalek M, Shogan BD, Defazio J, Flemming I, Shakhsheer B, Weber S, Landon E, Garcia-Houchins S, Siegel J, Alverdy J, Knight R, Stephens B, Gilbert JA. Bacterial colonization and succession in a newly opened hospital. Sci Transl Med 2017; 9:eaah6500. [PMID: 28539477 PMCID: PMC5706123 DOI: 10.1126/scitranslmed.aah6500] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/27/2017] [Indexed: 11/02/2022]
Abstract
The microorganisms that inhabit hospitals may influence patient recovery and outcome, although the complexity and diversity of these bacterial communities can confound our ability to focus on potential pathogens in isolation. To develop a community-level understanding of how microorganisms colonize and move through the hospital environment, we characterized the bacterial dynamics among hospital surfaces, patients, and staff over the course of 1 year as a new hospital became operational. The bacteria in patient rooms, particularly on bedrails, consistently resembled the skin microbiota of the patient occupying the room. Bacterial communities on patients and room surfaces became increasingly similar over the course of a patient's stay. Temporal correlations in community structure demonstrated that patients initially acquired room-associated taxa that predated their stay but that their own microbial signatures began to influence the room community structure over time. The α- and β-diversity of patient skin samples were only weakly or nonsignificantly associated with clinical factors such as chemotherapy, antibiotic usage, and surgical recovery, and no factor except for ambulatory status affected microbial similarity between the microbiotas of a patient and their room. Metagenomic analyses revealed that genes conferring antimicrobial resistance were consistently more abundant on room surfaces than on the skin of the patients inhabiting those rooms. In addition, persistent unique genotypes of Staphylococcus and Propionibacterium were identified. Dynamic Bayesian network analysis suggested that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse but that there were no universal patterns of transmission across patient rooms.
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Affiliation(s)
- Simon Lax
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Naseer Sangwan
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Daniel Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Larsen
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Kim M Handley
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
| | - Miles Richardson
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
| | - Kristina Guyton
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Monika Krezalek
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Benjamin D Shogan
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Jennifer Defazio
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Irma Flemming
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Baddr Shakhsheer
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Stephen Weber
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Emily Landon
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Sylvia Garcia-Houchins
- Department of Medicine, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA
| | - Jeffrey Siegel
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
- Dalla Lana School of Public Health, University of Toronto, 223 College Street, Toronto, Ontario M5T 1R4, Canada
| | - John Alverdy
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92037, USA
| | - Brent Stephens
- Department of Civil, Architectural and Environmental Engineering, Illinois Institute of Technology, 3201 South Dearborn Street, Chicago, IL 60616, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.
- Division of Biosciences, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Microbiome Center, Department of Surgery, University of Chicago, A27 South Maryland Avenue, Chicago, IL 60637, USA
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85
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Maritz JM, Sullivan SA, Prill RJ, Aksoy E, Scheid P, Carlton JM. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City. PLoS One 2017; 12:e0175527. [PMID: 28384336 PMCID: PMC5383295 DOI: 10.1371/journal.pone.0175527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
Abstract
Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.
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Affiliation(s)
- Julia M. Maritz
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Steven A. Sullivan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Robert J. Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, California, United States of America
| | - Emre Aksoy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Paul Scheid
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Jane M. Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
- * E-mail:
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86
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Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R. Microbiome Tools for Forensic Science. Trends Biotechnol 2017; 35:814-823. [PMID: 28366290 DOI: 10.1016/j.tibtech.2017.03.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 01/28/2023]
Abstract
Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics.
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Affiliation(s)
- Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Amina Bouslimani
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pieter Dorrestein
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Division of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI 96816, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, USA
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87
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The human microbiome, from Achilles armour to Nessus’ shirt. Arch Toxicol 2017; 91:2699-2701. [DOI: 10.1007/s00204-017-1951-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 02/27/2017] [Indexed: 12/27/2022]
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Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome. mBio 2017; 8:mBio.00093-17. [PMID: 28351915 PMCID: PMC5371408 DOI: 10.1128/mbio.00093-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hands play a critical role in the transmission of microbiota on one’s own body, between individuals, and on environmental surfaces. Effectively measuring the composition of the hand microbiome is important to hand hygiene science, which has implications for human health. Hand hygiene products are evaluated using standard culture-based methods, but standard test methods for culture-independent microbiome characterization are lacking. We sampled the hands of 50 participants using swab-based and glove-based methods prior to and following four hand hygiene treatments (using a nonantimicrobial hand wash, alcohol-based hand sanitizer [ABHS], a 70% ethanol solution, or tap water). We compared results among culture plate counts, 16S rRNA gene sequencing of DNA extracted directly from hands, and sequencing of DNA extracted from culture plates. Glove-based sampling yielded higher numbers of unique operational taxonomic units (OTUs) but had less diversity in bacterial community composition than swab-based sampling. We detected treatment-induced changes in diversity only by using swab-based samples (P < 0.001); we were unable to detect changes with glove-based samples. Bacterial cell counts significantly decreased with use of the ABHS (P < 0.05) and ethanol control (P < 0.05). Skin hydration at baseline correlated with bacterial abundances, bacterial community composition, pH, and redness across subjects. The importance of the method choice was substantial. These findings are important to ensure improvement of hand hygiene industry methods and for future hand microbiome studies. On the basis of our results and previously published studies, we propose recommendations for best practices in hand microbiome research. The hand microbiome is a critical area of research for diverse fields, such as public health and forensics. The suitability of culture-independent methods for assessing effects of hygiene products on microbiota has not been demonstrated. This is the first controlled laboratory clinical hand study to have compared traditional hand hygiene test methods with newer culture-independent characterization methods typically used by skin microbiologists. This study resulted in recommendations for hand hygiene product testing, development of methods, and future hand skin microbiome research. It also demonstrated the importance of inclusion of skin physiological metadata in skin microbiome research, which is atypical for skin microbiome studies.
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89
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Hampton-Marcell JT, Lopez JV, Gilbert JA. The human microbiome: an emerging tool in forensics. Microb Biotechnol 2017; 10:228-230. [PMID: 28244273 PMCID: PMC5328825 DOI: 10.1111/1751-7915.12699] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Jarrad T Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60443, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
- The Microbiome Center, University of Chicago, Chicago, IL, 60637, USA
| | - Jose V Lopez
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60443, USA
- The Microbiome Center, University of Chicago, Chicago, IL, 60637, USA
- Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
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90
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Barnard E, Li H. Shaping of cutaneous function by encounters with commensals. J Physiol 2017; 595:437-450. [PMID: 26988937 PMCID: PMC5233660 DOI: 10.1113/jp271638] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/05/2016] [Indexed: 01/17/2023] Open
Abstract
The skin is the largest organ in the human body and provides the first line of defence against environmental attack and pathogen invasion. It harbor multiple commensal microbial communities at different body sites, which play important roles in sensing the environment, protecting against colonization and infection of pathogens, and guiding the host immune system in response to foreign invasions. The skin microbiome is largely variable between individuals and body sites, with several core commensal members commonly shared among individuals at the healthy state. These microbial commensals are essential to skin health and can potentially lead to disease when their abundances and activities change due to alterations in the environment or in the host. While recent advances in sequencing technologies have enabled a large number of studies to characterize the taxonomic composition of the skin microbiome at various body sites and under different physiological conditions, we have limited understanding of the microbiome composition and dynamics at the strain level, which is highly important to many microbe-related diseases. Functional studies of the skin microbial communities and the interactions among community members and with the host are currently scant, warranting future investigations. In this review, we summarize the recent findings on the skin microbiome, highlighting the roles of the major commensals, including bacteria, fungi and bacteriophages, in modulating skin functions in health and disease. Functional studies of the skin microbiota at the metatranscriptomic and proteomic levels are also included to illustrate the interactions between the microbiota and the host skin.
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Affiliation(s)
- Emma Barnard
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of MedicineUCLACAUSA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of MedicineUCLACAUSA
- UCLA‐DOE Institute for Genomics and ProteomicsLos AngelesCAUSA
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91
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Wilkins D, Leung MHY, Lee PKH. Microbiota fingerprints lose individually identifying features over time. MICROBIOME 2017; 5:1. [PMID: 28086968 PMCID: PMC5234115 DOI: 10.1186/s40168-016-0209-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/22/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Humans host individually unique skin microbiota, suggesting that microbiota traces transferred from skin to surfaces could serve as forensic markers analogous to fingerprints. While it is known that individuals leave identifiable microbiota traces on surfaces, it is not clear for how long these traces persist. Moreover, as skin and surface microbiota change with time, even persistent traces may lose their forensic potential as they would cease to resemble the microbiota of the person who left them. We followed skin and surface microbiota within households for four seasons to determine whether accurate microbiota-based matching of individuals to their households could be achieved across long time delays. RESULTS While household surface microbiota traces could be matched to the correct occupant or occupants with 67% accuracy, accuracy decreased substantially when skin and surface samples were collected in different seasons, and particularly when surface samples were collected long after skin samples. Most OTUs persisted on skin or surfaces for less than one season, indicating that OTU loss was the major cause of decreased matching accuracy. OTUs that were more useful for individual identification persisted for less time and were less likely to be deposited from skin to surface, suggesting a trade-off between the longevity and identifying value of microbiota traces. CONCLUSIONS While microbiota traces have potential forensic value, unlike fingerprints they are not static and may degrade in a way that preferentially erases features useful in identifying individuals.
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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, B5423-AC1, Tat Chee Avenue, Kowloon, Hong Kong, Special Administrative Region of China
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92
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Dietrich M, Kearney T, Seamark ECJ, Markotter W. The excreted microbiota of bats: evidence of niche specialisation based on multiple body habitats. FEMS Microbiol Lett 2016; 364:fnw284. [DOI: 10.1093/femsle/fnw284] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/13/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
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Murgier J, Coste JF, Cavaignac E, Bayle-Iniguez X, Chiron P, Bonnevialle P, Laffosse JM. Microbial flora on cell-phones in an orthopedic surgery room before and after decontamination. Orthop Traumatol Surg Res 2016; 102:1093-1096. [PMID: 27836449 DOI: 10.1016/j.otsr.2016.09.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 09/05/2016] [Accepted: 09/19/2016] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Cell-phones are the typical kind of object brought into the operating room from outside by hospital staff. A great effort is made to reduce the level of potentially contaminating bacteria in the operating room, and introducing these devices may run counter to good practice. The study hypothesis was that cell-phones are colonized by several strains of bacteria and may constitute a source of nosocomial contamination. The main study objective was to screen for bacterial colonies on the surfaces of cell-phones introduced in an orthopedic surgery room. The secondary objective was to assess the efficacy of decontamination. MATERIAL AND METHOD Samples were taken from the cell-phones of hospital staff (surgeons, anaesthetists, nurses, radiology operators, and external medical representatives) entering the operating room of the university hospital center orthopedic surgery department, Toulouse (France). Sampling used Count Tact® contact gel, without wiping the phone down in advance. Both sides of the phone were sampled, before and after decontamination with a pad imbibed with 0.25% Surfanios® Premium disinfectant. A nasal sample was also taken to investigate the correlation between Staphylococcus aureus in the nasal cavities and on the cell-phone. RESULTS Fifty-two cell-phones were sampled. Before decontamination, the mean number of colony-forming units (CFU) was 258 per phone (range, 0-1,664). After decontamination, it was 127 (range, 0-800) (P=0.0001). Forty-nine cell-phones bore CFUs before decontamination (94%), and 39 after (75%) (P=0.02). DISCUSSION Cell-phones are CFU carriers and may thus lead to contamination. Guidelines should be drawn up to encourage cleaning phones regularly and to reduce levels of use within the operating room.
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Affiliation(s)
- J Murgier
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France.
| | - J-F Coste
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - E Cavaignac
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - X Bayle-Iniguez
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - P Chiron
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - P Bonnevialle
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - J-M Laffosse
- Service d'orthopédie-traumatologie, hôpital Pierre-Paul-Riquet, 308, avenue de Grande-Bretagne, 31059 Toulouse, France
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Corrin T, Lin J, MacNaughton C, Mahato S, Rajendiran A. The role of mobile communication devices in the spread of infections within a clinical setting. ACTA ACUST UNITED AC 2016. [DOI: 10.5864/d2016-014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mobile communication devices (MCDs) are routinely used in clinical settings. Bacterial contamination of MCDs is a growing concern as they can serve as a potential reservoir for infectious diseases. Recent studies have found that between 9% and 15% of MCDs carry pathogenic bacteria. To reduce contamination, recommendations are to practice good hand hygiene, restrict MCDs in high-risk areas, and sanitize MCDs using 70% isopropyl alcohol.
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Affiliation(s)
- Tricia Corrin
- Master of Public Health Program, University of Guelph, Guelph, ON, Canada. (All authors contributed equally to the paper.)
| | - Joanne Lin
- Master of Public Health Program, University of Guelph, Guelph, ON, Canada. (All authors contributed equally to the paper.)
| | - Catherine MacNaughton
- Master of Public Health Program, University of Guelph, Guelph, ON, Canada. (All authors contributed equally to the paper.)
| | - Sarah Mahato
- Master of Public Health Program, University of Guelph, Guelph, ON, Canada. (All authors contributed equally to the paper.)
| | - Aarabhi Rajendiran
- Master of Public Health Program, University of Guelph, Guelph, ON, Canada. (All authors contributed equally to the paper.)
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Leung MHY, Lee PKH. The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review. MICROBIOME 2016; 4:21. [PMID: 27216717 PMCID: PMC4877933 DOI: 10.1186/s40168-016-0165-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/11/2016] [Indexed: 05/10/2023]
Abstract
Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.
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Affiliation(s)
- Marcus H. Y. Leung
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
| | - Patrick K. H. Lee
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, B5423-AC1 Hong Kong
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Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C. Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems 2016; 1:e00018-16. [PMID: 27822528 PMCID: PMC5069760 DOI: 10.1128/msystems.00018-16] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/28/2016] [Indexed: 01/01/2023] Open
Abstract
Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs. Author Video: An author video summary of this article is available.
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Affiliation(s)
- Tiffany Hsu
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Regina Joice
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jose Vallarino
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Galeb Abu-Ali
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Afrah Shafquat
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Casey DuLong
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Dirk Gevers
- Broad Institute, Cambridge, Massachusetts, USA
| | | | - Xochitl C. Morgan
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - John D. Spengler
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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97
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Abstract
Humanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown. Humanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown. In their article in this issue, Chase and colleagues (J. Chase, J. Fouquier, M. Zare, D. L. Sonderegger, R. Knight, S. T. Kelley, J. Siegel, and J. G. Caporaso, mSystems 1(2):e00022-16, 2016, http://dx.doi.org/10.1128/mSystems.00022-16) present an office building study in which they controlled for environmental factors, geography, surface material, sampling location, and human interaction type. They found that surface location and geography were the strongest factors contributing to microbial community structure, while surface material had little effect. Even in the absence of direct human interaction, BE surfaces were composed of 25 to 30% human skin-associated taxa. The authors demonstrate how technical variation across sequencing runs is a major issue, especially in BE work, where the biomass is often low and the potential for PCR contaminants is high. Overall, the authors conclude that BE surfaces are desert-like environments where microbes passively accumulate.
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98
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Shi X, Xue C, Fang F, Song X, Yu F, Liu M, Wei Z, Fang X, Zhao D, Xin H, Wang X. Full Spectrum Visible LED Light Activated Antibacterial System Realized by Optimized Cu2O Crystals. ACS APPLIED MATERIALS & INTERFACES 2016; 8:8386-8392. [PMID: 26978589 DOI: 10.1021/acsami.6b00914] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Assisted by three-dimensional printing technology, we proposed and demonstrated a full spectrum visible light activated antibacterial system by using a combination of 500 nm sized Cu2O crystals and light-emitting diode (LED) lamps. Further improved antibacterial ratios were achieved, for the first time, with pure Cu2O for both Gram-positive bacteria and Gram-negative bacteria among all of the six different color LED lamps. For practical antibacterial applications, we revealed that the nonwoven fabric could act as excellent carrier for Cu2O crystals and provide impressive antibacterial performance. Furthermore, integrated with our self-developed app, the poly(ethylene terephthalate) film loaded with Cu2O crystals also showed significant antibacterial property, thus making it possible to be applied in field of touch screen. The present research not only provided a healthier alternative to traditional ultraviolet-based sterilization but also opened an auto-response manner to decrease the rate of microbial contamination on billions of touch screen devices.
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Affiliation(s)
- Xiaotong Shi
- Institute of Translational Medicine, NanChang University , NanChang, Jiangxi 330031, China
| | - Chaowen Xue
- Institute of Translational Medicine, NanChang University , NanChang, Jiangxi 330031, China
| | - Fang Fang
- National Engineering Technology Research Center for LED on Si Substrate, NanChang University , NanChang, Jiangxi 330047, China
| | - Xiangwei Song
- Institute of Translational Medicine, NanChang University , NanChang, Jiangxi 330031, China
| | - Fen Yu
- College of Chemistry, NanChang University , NanChang, Jiangxi 330031, China
| | - Miaoxing Liu
- College of Chemistry, NanChang University , NanChang, Jiangxi 330031, China
| | - Zhipeng Wei
- State Key Laboratory of High Power Semiconductor Laser of ChangChun University of Science and Technology , ChangChun, Jinlin 130022, China
| | - Xuan Fang
- State Key Laboratory of High Power Semiconductor Laser of ChangChun University of Science and Technology , ChangChun, Jinlin 130022, China
| | - Dongxu Zhao
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences , ChangChun, Jilin 130033, China
| | - Hongbo Xin
- Institute of Translational Medicine, NanChang University , NanChang, Jiangxi 330031, China
| | - Xiaolei Wang
- Institute of Translational Medicine, NanChang University , NanChang, Jiangxi 330031, China
- College of Chemistry, NanChang University , NanChang, Jiangxi 330031, China
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99
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Hoisington AJ, Brenner LA, Kinney KA, Postolache TT, Lowry CA. The microbiome of the built environment and mental health. MICROBIOME 2015; 3:60. [PMID: 26674771 PMCID: PMC4682225 DOI: 10.1186/s40168-015-0127-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/29/2015] [Indexed: 05/20/2023]
Abstract
The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is little knowledge of the impacts of the MoBE on mental health. Depending on the specific microbial species involved, the transfer of microorganisms from the built environment to occupant's cutaneous or mucosal membranes has the potential to increase or disrupt immunoregulation and/or exaggerate or suppress inflammation. Preclinical evidence highlighting the influence of the microbiota on systemic inflammation supports the assertion that microorganisms, including those originating from the built environment, have the potential to either increase or decrease the risk of inflammation-induced psychiatric conditions and their symptom severity. With advanced understanding of both the ecology of the built environment, and its influence on the human microbiome, it may be possible to develop bioinformed strategies for management of the built environment to promote mental health. Here we present a brief summary of microbiome research in both areas and highlight two interdependencies including the following: (1) effects of the MoBE on the human microbiome and (2) potential opportunities for manipulation of the MoBE in order to improve mental health. In addition, we propose future research directions including strategies for assessment of changes in the microbiome of common areas of built environments shared by multiple human occupants, and associated cohort-level changes in the mental health of those who spend time in the buildings. Overall, our understanding of the fields of both the MoBE and influence of host-associated microorganisms on mental health are advancing at a rapid pace and, if linked, could offer considerable benefit to health and wellness.
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Affiliation(s)
- Andrew J Hoisington
- Department of Civil and Environmental Engineering, US Air Force Academy, 2354 Fairchild Dr. Suite 6H-161, Colorado Springs, CO, 80840, USA.
| | - Lisa A Brenner
- Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), University of Colorado Anschutz Medical Campus, 1055 Clermont Street, Denver, CO, 80220, USA.
| | - Kerry A Kinney
- Civil, Architectural and Environmental Engineering, University of Texas Austin, 402 E. Dean Keeton Street, Austin, TX, 78712-1085, USA.
| | - Teodor T Postolache
- University of Maryland School of Medicine, Baltimore MD, Rocky Mountain MIRECC and VISN 5 MIRECC, 685 W. Baltimore Street, Baltimore, MD, 21201, USA.
| | - Christopher A Lowry
- Department of Integrative Physiology and Center for Neuroscience, University of Colorado Boulder, 1725 Pleasant Street, Boulder, CO, 80309-0354, USA.
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100
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Miletto M, Lindow SE. Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences. MICROBIOME 2015; 3:61. [PMID: 26653310 PMCID: PMC4674937 DOI: 10.1186/s40168-015-0128-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/29/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building. RESULTS Indoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air. CONCLUSIONS Indoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics.
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Affiliation(s)
- Marzia Miletto
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
| | - Steven E Lindow
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
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